High genetic diversity of in situ and ex situ populations of Madagascan coffee species: Further implications for the management of coffee genetic resources

Tree Genetics and Genomes

Volumn 9, Issue 5, 2013, Pages 1295-1312

  Andrianasolo, Domohina N ^a   Davis, Aaron P ^b   Razafinarivo, Norosoa J ^c   Hamon, Serge ^c   Rakotomalala, Jean Jacques ^d   Sabatier, Sylvie Annabel ^a   Hamon, Perla ^c  

^a CIRAD   (France)

^b ROYAL BOTANIC GARDENS   (United Kingdom)

^c INSTITUT DE RECHERCHE POUR LE DÉVELOPPEMENT   (France)

^d FOFIFA   (Madagascar)

Author keywords

Coffea; Conservation; Genetic diversity; Genetic resources; Madagascar; Microsatellite markers

Indexed keywords

COFFEA;

EID: 84884416855     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-013-0638-4     Document Type: Article

References (43)

1. Anthony F, Dussert S, Dulloo E (2007) Coffee genetic resources. In: Engelmann F, Dulloo E, Astorga C et al (eds) Complementary strategies for ex situ conservation of coffee (Coffea arabica L.) genetic resources. A case study in CATIE, Costa Rica, Topical reviews in Agricultural Biodiversity. Bioversity International, Rome, pp 12-22.
2. Bretz F, Hothorn T, Westfall P (2010) Multiple comparisons using R. CRC Boca Raton R. 2. 11. 1 http://cran. r-project. org. Accessed 31 May 2010.
3. Brookfield JFY (1996) Genetic evidence for repression of somatic P element movements in Drosophila melanogaster consistent with a role for the KP element. Heredity 76(4): 384-391.
4. Brown AHD (1989) Core collections: a practical approach to genetic resources management. Genome 31: 818-824.
5. Charrier A (1978) La structure génétique des caféiers spontanés de la région malgache (Mascarocoffea): leur relation avec les caféiers d'origine africaine (Eucoffea). PhD Thesis Edn ORSTOM, Paris, 224 p.
6. Cubry P, Musoli P, Legnate H, Pot D, de Bellis F, Poncet V, Anthony F, Dufour M, Leroy T (2008) Diversity in coffee assessed with SSR markers: structure of the genus Coffea and perspectives for breeding. Genome 51: 50-63.
7. Davis AP (2010) Six species of Psilanthus transferred to Coffea (Coffeeae. Rubiaceae). Phytotaxa 10: 41-45.
8. Davis AP (2011) Psilanthus mannii, the type species of Psilanthus, transferred to Coffea. Nord J Bot 29: 471-472.
9. Davis AP, Govaerts R, Bridson DM, Stoffelen P (2006) An annotated taxonomic conspectus of the genus Coffea (Rubiaceae). Bot J Linn Soc 152: 465-512.
10. Davis AP, Tosh J, Ruch N, Fay M (2011) Growing coffee: Psilanthus (Rubiaceae) subsumed on the basis of molecular and morphological data; implications for the size, morphology, distribution and evolutionary history of Coffea. Bot J Linn Soc 167: 357-377.
11. de Kochko A, Akaffou S, Andrade AC, Campa C, Crouzillat D, Guyot R, Hamon P, Ming R, Mueller LA, Poncet V, Tranchant-Dubreuil C, Hamon S (2010) Advances in Coffea genomics. Adv Bot Res 53: 23-63. doi: 10. 1016/S0065-2296(10)53002.
12. Dulloo ME, Ebert AW, Dussert S, Gotor E, Astorg C, Vasquez N, Rakotomalala J-J, Rabemiafara A, Eira M, Bellachew B, Omondi C, Engelmann F, Anthony F, Watts J, Qamar Z, Snook L (2009) Cost efficiency of cryopreservation as a long-term conservation method for coffee genetic resources. Crop Sci vol 49: 2123-2138. doi: 10. 2135/cropsci2008. 12. 0736.
13. Dulloo ME, Guarino L, Engelmann F, Maxted N, Newbury J- H, Attere F, Ford-Lloyd BV (1998) Complementary conservation strategies for the genus Coffea: a case study of Mascarene Coffea species. Genet Resour Crop Evol 45: 565-579.
14. Dulloo ME, Hunter D, Borelli T (2010) Ex situ and in situ conservation of agricultural biodiversity: major advances and research needs. Notulae Botanicae Horti Agrobotanici Cluj-Napoca 38 no 2. Available at: http://notulaebotanicae. ro/nbha/article/view/4878/4522. Accessed 11 October 2011.
15. Engelmann F, Dulloo ME, Astorga C, Dussert S, Anthony F (2007) Conserving coffee genetic resources: complementary strategies for ex situ conservation of coffee (Coffea arabica L.) genetic resources. A case study in CATIE. Costa Rica, Biodiversity International, Rome, Italy, 61 p.
16. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611-2620. doi: 10. 1111/j. 1365-294X. 2005. 02553. x.
17. Excoffier L, Lischer HEL (2010) Arlequin suite ver 3. 5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10: 564-567.
18. Gomez C, Batti A, Le Pierre D, Campa C, Hamon S, de Kochko A, Hamon P, Huynh F, Despinoy M, Poncet V (2010) Favourable habitats for Coffea inter-specific hybridization in central New Caledonia: combined genetic and spatial analyses. J Appl Ecol 47: 85-95. doi: 10. 1111/j. 1365-2664. 2009. 01762. x.
19. Gomez C, Dussert S, Hamon P, Hamon S, Kochko A, Poncet V (2009) Current genetic differentiation of Coffea canephora Pierre ex A. Froehn in the Guineo-Congolian African zone: cumulative impact of ancient climatic changes and recent human activities. BMC Evol Biol 9: 167.
20. Goudet J (1995) FSTAT Version 1. 2: a computer program to calculate F-statistics. J Hered 86: 485-486.
21. Hamon P, Duroy PO, Dubreuil-Tranchant C, Costa PMA, Duret C, Razafinarivo NJ, Couturon E, Hamon S, de Kochko A, Poncet V, Guyot R (2011) Two novel Ty1-copia retrotransposons isolated from coffee trees can effectively reveal evolutionary relationships in the Coffea genus (Rubiaceae). Mol Genet Genom 285: 447-460.
22. Hamon S, Dussert S, Deu M, Hamon P, Seguin M, Glaszmann JC, Grivet L, Chantereau J, Chevallier M-H, Flori A, Lashermes P, Legnate H, Noirot M (1998) Effects of quantitative and qualitative principal component score strategies on the structure of coffee, rice, rubber tree and sorghum core collections. Genet Select Evol 30: 237-258.
23. Hawkes JG, Maxted N, Ford-Lloyd BV (2001) The ex situ conservation of plant genetic resources. Kluwer Academic Publishers, Dordrecht, p 250.
24. Hendre PS, Phanindranath R, Annapurna V, Lalremruata A, Aggarwal RK (2008) Development of new genomic microsatellite markers from robusta coffee (Coffea canephora Pierre ex A. Froehner) showing broad cross-species transferability and utility in genetic studies. BMC Plant Biol 8: 51-69.
25. Holmgren PK, Holmgren NH, Barnett LC (1990) Index herbariorum. Part 1: The herbaria of the world, 8th edn. New York Botanical Garden, Bronx, New York, 693 p.
26. International Coffee Organization (ICO) (2012) World Coffee Trade [http://www. ico. org/trade_e. asp?section=About_Coffee] Accessed 12 September 2012.
27. IUCN (2001) IUCN red list categories, version 3. 1. Gland/Cambridge: IUCN Species Survival Commission.
28. Krishnan S, Ranker TA, Davis AP, Rakotomalala J-J (2013a) The study of genetic diversity patterns of Coffea commersoniana, an endangered coffee species from Madagascar: a model for conservation of other littoral forest species. Tree Genet Genomes 9: 179-187. doi: 10. 1007/s11295-012-0545-0.
29. Krishnan S, Ranker TA, Davis AP, Rakotomalala J-J (2013b) An assessment of the genetic integrity of ex situ germplasm collections of three endangered species of Coffea from Madagascar: implications for the management of field germplasm collections. Genet Resour Crop Evol 60: 1021-1036. doi: 10. 1007/s10722-012-9898-3.
30. Lefebvre-Pautigny F, Wu F, Philippot M, Rigoreau M, Priyono ZM, Frasse P, Bouzayen M, Broun P, Pétiard V, Tanksley SD, Crouzillat D (2010) High resolution synteny maps allowing direct comparisons between the coffee and tomato genomes. Tree Genet Genomes 6: 565-577. doi: 10. 1007/s11295-010-0272-3.
31. Maurin O, Davis AP, Chester M, Mvungi EF, Jaufeerally-Fakim Y, Fay MF (2007) Towards a phylogeny for Coffea (Rubiaceae): identifying well-supported lineages based on nuclear and plastid DNA sequences. Ann Bot 100: 1565-1583.
32. Patterson N, Price AL, Reich D (2006) Population structure and eigen analysis. PLoS Genet 2(12): e190. doi: 10. 1371/journal. pgen. 0020190.
33. Peakall R, Smouse PE (2006) Genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6: 288-295. doi: 10. 1111/j. 1471-8286. 2005. 01155. x.
34. Plechakova O, Tranchant-Dubreuil C, Benedet F, Couderc M, Tinaut A, Viader V, De Block P, Hamon P, Campa C, de Kochko A, Hamon S, Poncet V (2009) MoccaDB -an integrative database for functional. Comparative and diversity studies in the Rubiaceae family. BMC Plant Biol 9(1): 123.
35. Poncet V, Hamon P, Minier J, Carasco C, Hamon S, Noirot M (2004) SSR cross-amplification and variation within coffee trees (Coffea spp.). Genome 47: 1071-1081.
36. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
37. Rakotomalala JJ (1992) Diversité biochimique des caféiers: Analyse des acides hydroxycinnamiques, bases puriques et diterpènes glycosides. Particularités des caféiers sauvages de la région malgache (Mascarocoffea Chev.). Thesis, Collection TDM, ORSTOM, Paris.
38. Razafinarivo NJ, Guyot R, Davis AP, Couturon C, Hamon S, Crouzillat D, Rigoreau M, Dubreuil-Tranchant C, Poncet V, De Kochko A, Rakotomalala J-J, Hamon P (2013) Genetic structure and diversity of coffee (Coffea) across Africa and the Indian Ocean islands revealed using microsatellites. Ann Bot 111: 229-248.
39. Reed BM, Engelmann F, Dulloo ME, Engels JMM (2004) Technical guidelines for the management of field and in vitro germplasm collections. Handbook for genebanks No. 7. IPGRI/SGRP, Italy-Rome.
40. Royal Botanic Gardens, Kew (2008) Seed Information Database (SID) Version 7. 1 Available from: http://data. kew. org/sid/ (May 2008).
41. Silvestrini M, Junqueira MG, Favarin AC, Guerreiro-Filho O, Maluf MP, Silvarolla MB, Colombo CA (2007) Genetic diversity and structure of Ethiopian. Yemen and Brazilian Coffea arabica L. accessions using microsatellite markers. Genet Resour Crop Evol 54: 1367-1379.
42. Shorthouse DP (2013). SimpleMappr, an online tool to produce publication-quality point maps. www. simplemappr. net accessed 1 Jan 2013.
43. van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) Micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4: 535-5.